Research Description

Fundamental Mechanisms of Molecular Self-Assembly

Understanding and ultimately controlling how molecules assemble into functional structures is critical in fields ranging from materials science and chemistry to structural and cell biology. We have a long-standing interest in understanding the fundamental mechanisms of self-assembly, ranging from the self-association of dye molecules into excitonic structures, to protein and peptide aggregation, both in solution and at model interfaces. Our most recent work has focused on the dynamics of molecular assembly in live cells and specifically how the hetero- and homo-geneous association of membrane receptors impacts cell signaling and cell-cell interactions.

Determining the structural and conformational requirements for these complex assembly processes, and the dynamics thereof, is best accomplished by examining these phenomena on the molecular scale, in real-time, and under nominally real-world conditions. We have therefore focused on the design and optimization of combinatorial microscopies for the direct interrogation of molecular and biomolecular self-assembly. This has resulted in several platforms with unique capabilities for assessing the role of orientation, conformation, and structure on self-assembly over several orders of magnitude in both length and time.

These platforms have allowed us to

1. identify the critical dimensions associated with exciton generation in two-dimensional molecular solids
2. assess how protein and peptide sequence alter the dynamics of membrane association and disruption
3. determine the spatial, conformational, and dynamic heterogeneity of membrane receptors in live cells
4. interrogate in situ complex formation during mitochondrial membrane remodeling.

Studies of BIomolecular Self-Assembly

Toxins may exert their influence through pore complexes or other mechanisms of membrane disruption. Antimicrobial (AMP) or cell-penetrating peptides (CPP) necessarily need to pass through the membrane in order to exert their action. Intrinsic membrane proteins may require specific intermolecular interactions with specific lipids or other membrane components or structures in order to exert their function. Understanding how proteins orient, associate, and interact at a membrane interface is fundamental to understanding their function, disease progression, and devising therapeutic strategies.

The following questions need to be addressed in order to understand, control, and exploit protein-membrane interactions:

1. What controls the association of a protein to a membrane?
2. What changes take place upon association? Is there a change in molecular shape or orientation? How do such changes impact functionality? What is the effect on the membrane itself? Does membrane restructuring occur?
3. How quickly does this happen?
4. How many molecules are involved and are other molecules recruited?
5. Where do these interactions occur? Are they dependent on membrane structure and composition and if so, what are the critical components?

Membranes can also act as templates or substrates for assembly. We are investigating the role of membrane chemistry, local structure and phase, and composition on the templated growth of novel dye aggregates. By rationally controlling the substrate structure and / or the dye chemistry, new supramolecular architectures may be generated that give rise to novel optical properties.

Single Molecule Imaging Tools and Techniques

While conventional techniques such as spectroscopy and crystallography have provided remarkable insights into biomolecular structure-function relationships, recent developments in in situ single molecule functional imaging tools are providing researchers with the unique opportunity to perform correlated characterization of protein interactions, often in real-time, and under physiologically relevant conditions, on molecular length scales.

Adapting these tools for imaging live cells, and providing direct insights into trafficking, signaling, and characterization of cellular dynamics, on single molecule length scales will provide critical new insights into the molecular mechanisms of disease and protein-protein interaction networks.

Building on the theme of combinatorial microscopies, which describes techniques that combine two or more characteristics of light (wavelength, polarization, frequency) with other imaging modalities, we are developing a platform of single molecule hyperspectral imaging tools that will enable us directly characterize protein structure and assembly, enable in situ measurement of protein association forces, and directly determine the kinetics of complex formation in live cells.

Computational Biophysics

Complementing our experimental approaches are computational techniques that can offer atomistic insights into protein-protein interactions and molecular conformations. Using all-atom molecular dynamics simulations, we are

• characterizing the forces associated with protein unfolding, in direct analogy to single molecule force spectroscopy experiments;
• studying peptide-membrane interactions, which is important for understanding how toxins and antimicrobial peptides interact with cell membranes;

By using these approaches in both predictive and retrospective approaches, we can assess, in silico, the role of peptide chemistry, membrane composition, and unfolding rates and forces on the dynamics of protein-protein interactions.

Publications

View all publications on PubMed